The alien was bored, and decided he needed new friends. He finally decides to head to a new place he's been watching, Roanoke.
The alien finally meets the colonists. He makes the choice to abduct them. He makes sure that there is NOTHING left behind, and hides all signs of any struggle or violence he had to use to get them in his ship.
When John White comes back he realizes that this is the only logical solution, since the soil was fertile, and the native Americans around them were friendly, and wouldn't hurt the colonists.